GEO DataSets

(Submitter supplied) Genomic information from human patient samples of pediatric neuroblastoma cancers and known outcomes have led to specific gene lists put forward as high risk for disease progression. However, the reliance on gene expression correlations rather than mechanistic insight has shown limited potential and suggests a critical need for molecular network models that better predict neuroblastoma progression. In this study, we construct and simulate a molecular network of developmental genes and downstream signals in a 6-gene input logic model that predicts a favorable/unfavorable outcome based on the outcome of the four cell states including cell differentiation, proliferation, apoptosis, and angiogenesis. We simulate the mis-expression of the tyrosine receptor kinases, trkA and trkB, two prognostic indicators of neuroblastoma, and find differences in the number and probability distribution of steady state outcomes. We validate the mechanistic model assumptions using RNAseq of the SHSY5Y human neuroblastoma cell line to define the input states and confirm the predicted outcome with antibody staining. Lastly, we apply input gene signatures from 77 published human patient samples and show that our model makes more accurate disease outcome predictions for early stage disease than any current neuroblastoma gene list. These findings highlight the predictive strength of a logic-based model based on developmental genes and offer a better understanding of the molecular network interactions during neuroblastoma disease progression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

3 Samples

Download data: TXT

(Submitter supplied) Single-color gene expression profiles from 3 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. To gain insights into the molecular processes occurring upon FOXP1 re-expression, we performed series of time-resolved gene expression measurements in FOXP1 and GFP transgenic neuroblastoma cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16876

24 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL570 GPL2004

53 Samples

Download data: CEL

(Submitter supplied) Gene expression analysis was performed on 30 Neuroblastomas to identify genes whose transcription is significantly altered by recurrent chromosomal alterations. Genomic copy number losses and gains had been delineated in the tumours using FISH and SNP arrays. We have identified genes significantly altered by 7 recurrent alterations: 1p, 3p, 4p, 10q and 11q loss, 2p and 17q gain, and genes co-amplified and over-expressed as a result of MYCN amplification. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL2004

23 Samples

Download data: CEL

(Submitter supplied) Gene expression analysis was performed on 30 Neuroblastomas to identify genes whose transcription is significantly altered by recurrent chromosomal alterations. Genomic copy number losses and gains had been delineated in the tumours using FISH and SNP arrays. We have identified genes significantly altered by 7 recurrent alterations: 1p, 3p, 4p, 10q and 11q loss, 2p and 17q gain, and genes co-amplified and over-expressed as a result of MYCN amplification. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

30 Samples

Download data: CEL

(Submitter supplied) The number of long-term survivors of high-risk neuroblastoma remains discouraging, with 10-year survival as low as 20%, despite decades of considerable international efforts to improve outcome. Major obstacles remain and include managing resistance to induction therapy, which causes tumor progression and early death in high-risk patients, and managing chemotherapy-resistant relapses, which can occur years after the initial diagnosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

36 Samples

Download data: TXT

(Submitter supplied) We studied transcriptional changes by Illumina HumanHT-12 v4 microarrays in 2 Neuroblastoma cell lines after i-BET-726 treatment

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS5364 GDS5365

Platform:

GPL10558

18 Samples

Download data: TXT

Analysis of SK-N-SH neuroblastoma (NB) cells treated with 0.1 or 1 uM I-BET726, a BET inhibitor. MYCN is unamplified in SK-N-SH. BET inhibitors display anti-proliferative activity in MYC driven hematologic cancer models. Results provide insight into the anti-proliferative activity of I-BET726 in NB.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 agent, 3 dose sets

Platform:

GPL10558

Series:

GSE47386

9 Samples

Download data

Analysis of CHP-212 neuroblastoma (NB) cells treated with 0.1 or 1 uM I-BET726, a BET inhibitor. MYCN is amplified in CHP-212. BET inhibitors display anti-proliferative activity in MYC driven hematologic cancer models. Results provide insight into the anti-proliferative activity of I-BET726 in NB.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 agent, 3 dose sets

Platform:

GPL10558

Series:

GSE47386

9 Samples

Download data

(Submitter supplied) Single-color gene expression profiles from 649 neuroblastoma tumors were generated using 44K oligonucleotide microarrays. We aimed at determining the association of class I HOX gene expression patterns with prognostic markers in neuroblastoma.We investigated the functional consequences of HOXC9 re-expression on neuroblastoma growth and programmed cell death. One-color gene expression analysis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16876

649 Samples

Download data: TXT

(Submitter supplied) Single-color gene expression profiles from 2 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. To gain insights into the molecular processes occurring upon HOXC9 re-expression, we analyzed gene expression profiles of IMR-32 and SK-N-AS cells after Hox-C9 induction using microarrays. We used gene ontology (GO) annotations to find classes of genes that are significantly over-represented in gene sets that were either up- or downregulated after HOXC9 re-expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16876

24 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by array; Expression profiling by array

6 related Platforms

881 Samples

Download data: TXT

(Submitter supplied) Oligonucleotide aCGH profiles from 209 neuroblastoma tumor samples were generated using 44K, 105K or 1M microarrays. The 209th sample is represented by Sample GSM634116.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL4093

123 Samples

Download data: TXT

(Submitter supplied) Oligonucleotide aCGH profiles from 209 neuroblastoma tumor samples were generated using 44K, 105K or 1M microarrays. The 209th sample is represented by Sample GSM634116.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL8736

9 Samples

Download data: TXT

(Submitter supplied) Oligonucleotide aCGH profiles from 209 neuroblastoma tumor samples were generated using 44K, 105K or 1M microarrays. The 209th sample is represented by Sample GSM634116.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL16865 GPL8355 GPL2873

76 Samples

Download data: TXT

(Submitter supplied) Single-color gene expression profiles from IMR-32 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. To gain insights into the molecular processes occurring upon TFAP2B re-expression, we performed gene expression measurements in TFAP2B and GFP expressing transgenic IMR-32 neuroblastoma cell lines at d2 and d7 of transgene induction.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16876

4 Samples

Download data: TXT

(Submitter supplied) Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining public microarray and RNA sequencing datasets, we identified neuroblastoma highly expressed 1 (NHEG1) as a novel 1360-bp lncRNA associated with poor outcome of NB. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

6 Samples

Download data: CEL

(Submitter supplied) Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of publically available microarray datasets, we discovered a novel 963-bp lncRNA, named FOXD3 antisense RNA 1 (FOXD3-AS1), as an independent prognostic marker for favorable clinical outcome of NB patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array

Platforms:

GPL570 GPL9202

5 Samples

Download data: CEL, TXT

(Submitter supplied) Title: Array-based gene expression, CGH and tissue data define a 12q24 gain in neuroblastic tumors with prognostic implication. Background: Neuroblastoma has successfully served as a model system for the identification of neuroectoderm-derived oncogenes. However, in spite of various efforts, only a few clinically useful prognostic markers have been found. Here, we present a framework, which integrates DNA, RNA and tissue data to identify and prioritize genetic events that represent clinically relevant new therapeutic targets and prognostic biomarkers for neuroblastoma. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9202

2 Samples

Download data: TXT